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| 16428279 | The open nucleotide pocket of the profilin/actin x-ray structure is unstable and closes in the absence of profilin. | Biophysical Journal | 2006 |
| 16458552 | Automatic atom type and bond type perception in molecular mechanical calculations. | J Mol Graph Model | 2006 |
| 16805629 | New-generation amber united-atom force field. | J Phys Chem B | 2006 |
| 16496993 | Chelate effect in cyclodextrin dimers: a computational (MD, MM/PBSA, and MM/GBSA) study. | Journal of Organic Chemistry | 2006 |
| 15801834 | Hierarchical database screenings for HIV-1 reverse transcriptase using a pharmacophore model, rigid docking, solvation docking, and MM-PB/SA. | Journal of Medicinal Chemistry | 2005 |
| 15099837 | Enhanced ab initio protein folding simulations in Poisson-Boltzmann molecular dynamics with self-guiding forces. | Journal of Molecular Graphics and Modelling | 2004 |
| 15376253 | Prediction of pKa shifts in proteins using a combination of molecular mechanical and continuum solvent calculations. | Journal of Computational Chemistry | 2004 |
| 15116359 | Development and testing of a general amber force field. | J Comput Chem | 2004 |
| 12579577 | Free energy calculations for theophylline binding to an RNA aptamer: Comparison of MM-PBSA and thermodynamic integration methods. | Biopolymers | 2003 |
| 12483674 | The intramolecular mechanism for the second proton transfer in triosephosphate isomerase (TIM): a QM/FE approach. | Journal of Computational Chemistry | 2003 |
| 12868101 | Direct hydroxide attack is a plausible mechanism for amidase antibody 43C9. | Journal of Computational Chemistry | 2003 |
| 14667217 | Investigation of neuraminidase-substrate recognition using molecular dynamics and free energy calculations. | Journal of Medicinal Chemistry | 2003 |
| 14531054 | A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. | J Comput Chem | 2003 |
| 12730601 | Closing of the nucleotide pocket of kinesin-family motors upon binding to microtubules. | Science | 2003 |
| 11979516 | Conformational preferences of substituted prolines in the collagen triple helix. | Biopolymers | 2002 |
| 11906282 | Molecular dynamics and free energy analyses of cathepsin D-inhibitor interactions: insight into structure-based ligand design. | J Med Chem | 2002 |
| 12395425 | pKa, MM, and QM studies of mechanisms of beta-lactamases and penicillin-binding proteins: acylation step. | Journal of Computational Chemistry | 2002 |
| 11895399 | Theoretical and experimental studies of biotin analogues that bind almost as tightly to streptavidin as biotin. | Journal of Organic Chemistry | 2002 |
| 12381197 | Molecular dynamics simulation study of the negative correlation in antibody AZ28-catalyzed oxy-cope rearrangement. | Journal of the American Chemical Society | 2002 |
| 11806909 | A classical and ab initio study of the interaction of the myosin triphosphate binding domain with ATP. | Biophysical Journal | 2002 |
| 12001225 | Simulating proteins at constant pH: An approach combining molecular dynamics and Monte Carlo simulation. | Proteins: Structure, Function and Bioinformatics | 2002 |
| 11913381 | Computational alanine scanning of the 1:1 human growth hormone-receptor complex. | Journal of Computational Chemistry | 2002 |
| 11222280 | Molecular dynamics study of the energetic, mechanistic, and structural implications of a closed phosphate tube in ncd. | Biophysical Journal | 2001 |
| 18428877 | Molecular modeling of nucleic acid structure: electrostatics and solvation. | Current Protocols in Nucleic Acid Chemistry | 2001 |
| 18428876 | Molecular modeling of nucleic acid structure: energy and sampling. | Current Protocols in Nucleic Acid Chemistry | 2001 |
| 18428873 | Molecular modeling of nucleic acid structure. | Current Protocols in Nucleic Acid Chemistry | 2001 |
| 18428869 | Molecular modeling of nucleic acid structure: setup and analysis. | Current Protocols in Nucleic Acid Chemistry | 2001 |
| 11536355 | Molecular dynamics simulations of a highly charged peptide from an SH3 domain: possible sequence-function relationship. | Proteins: Structure, Function and Bioinformatics | 2001 |
| 11591346 | Free-energy calculations highlight differences in accuracy between X-ray and NMR structures and add value to protein structure prediction. | Structure | 2001 |
| 11457384 | Use of MM-PBSA in reproducing the binding free energies to HIV-1 RT of TIBO derivatives and predicting the binding mode to HIV-1 RT of efavirenz by docking and MM-PBSA. | J Am Chem Soc | 2001 |
| 11457149 | An analysis of the interactions between the Sem-5 SH3 domain and its ligands using molecular dynamics, free energy calculations, and sequence analysis. | J Am Chem Soc | 2001 |
| 11456657 | 2.1 and 1.8 A average C(alpha) RMSD structure predictions on two small proteins, HP-36 and s15. | J Am Chem Soc | 2001 |
| 11384247 | Metabolism of sirolimus and its derivative everolimus by cytochrome P450 3A4: insights from docking, molecular dynamics, and quantum chemical calculations. | Journal of Medicinal Chemistry | 2001 |
| 11381525 | State of the art in studying protein folding and protein structure prediction using molecular dynamics methods. | Journal of Molecular Graphics and Modelling | 2001 |
| 11812257 | Molecular recognition by beta-cyclodextrin derivatives: FEP vs MM/PBSA study. | Combinatorial Chemistry and High Throughput Screening | 2001 |
| 11752442 | Computational study of protein specificity: the molecular basis of HIV-1 protease drug resistance. | Proc Natl Acad Sci U S A | 2001 |
| 11749542 | An alternative explanation for the catalytic proficiency of orotidine 5'-phosphate decarboxylase. | Journal of the American Chemical Society | 2001 |
| 11371457 | Molecular dynamics and binding specificity analysis of the bovine immunodeficiency virus BIV Tat-TAR complex. | Biophys J | 2001 |
| 11800566 | Molecular dynamics in the endgame of protein structure prediction. | J Mol Biol | 2001 |
| 11272701 | Does a diol cyclic urea inhibitor of HIV-1 protease bind tighter than its corresponding alcohol form? A study by free energy perturbation and continuum electrostatics calculations. | Journal of Computer-Aided Molecular Design | 2001 |
| 11170358 | Elucidating the nature of enzyme catalysis utilizing a new twist on an old methodology: quantum mechanical-free energy calculations on chemical reactions in enzymes and in aqueous solution. | Accounts of Chemical Research | 2001 |
| 11169394 | Computed free energy differences between point mutations in a collagen-like peptide. | Biopolymers | 2001 |
| 11340059 | Biomolecular simulations: recent developments in force fields, simulations of enzyme catalysis, protein-ligand, protein-protein, and protein-nucleic acid noncovalent interactions. | Annu Rev Biophys Biomol Struct | 2001 |
| 11031289 | Molecular dynamics simulation of nucleic acids. | Annual Review of Physical Chemistry | 2000 |
| 10764579 | Structure and thermodynamics of RNA-protein binding: using molecular dynamics and free energy analyses to calculate the free energies of binding and conformational change. | Journal of Molecular Biology | 2000 |
| 11025549 | Exhaustive mutagenesis in silico: multicoordinate free energy calculations on proteins and peptides. | Proteins: Structure, Function and Bioinformatics | 2000 |
| 11020294 | Binding of a diverse set of ligands to avidin and streptavidin: an accurate quantitative prediction of their relative affinities by a combination of molecular mechanics and continuum solvent models. | Journal of Medicinal Chemistry | 2000 |
| 10623503 | Investigating the binding specificity of U1A-RNA by computational mutagenesis. | Journal of Molecular Biology | 2000 |
| 10813813 | Use of MM-PB/SA in estimating the free energies of proteins: application to native, intermediates, and unfolded villin headpiece. | Proteins: Structure, Function and Bioinformatics | 2000 |
| 11123888 | Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. | Acc Chem Res | 2000 |